Born in Chambéry, Emmanuel Philibert was the only child of Charles III, Duke of Savoy and Beatrice of Portugal to reach adulthood. His mother was sister-in-law to Charles V, Holy Roman Emperor, and the future duke served in Charles's army during the war against Francis I of France, distinguishing himself by capturing Hesdin in July 1553. A month later, he became duke on the death of his father, but this was a nearly empty honour, as the vast majority of his hereditary lands had been occupied and administered by the French since 1536. Instead, he continued to serve the Habsburgs in hopes of recovering his lands, and served his maternal first cousin King Philip II as Governor of the Netherlands from 1555-1559.
In this capacity he personally led the Spanish invasion of northern France and won a brilliant victory at Saint-Quentin in August 1557. He was a suitor to Queen Elizabeth I when her sister Queen Mary of England was ruling. He had barely any money at that time.
By the Peace of Cateau Cambrésis between France and Spain, (1559) the duchy was restored to Emmanuel Philibert and he married his half-first cousin once removed Margaret of France, Duchess of Berry (1523-1574), daughter of King Francis I of France and sister to King Henry II. Their only child was Charles Emmanuel I of Savoy.
Emmanuel Philibert spent his rule regaining what had been lost in the costly wars with France. A skilled political strategist, he took advantage of various squabbles in Europe to slowly regain territory from both the French and the Spanish, including the city of Turin. He also purchased two territories. Internally, he moved the capital of the duchy from Chambéry to Turin and replaced Latin as the duchy's official language with Italian. He was attempting to acquire the marquisate of Saluzzo when he died in Turin.